Does it not make more sense to use clean, filtered water to transfer the heat out into the ocean? The heat exchanger can sit in the ocean to facilitate removing heat without the worry of having jellyfish clogging filters. Effective cooling capacity might be reduced without an active water stream going over the heat exchanger, but this can be compensated for by using a larger one.
The only possible problem I can see is the build-up of aquatic life on the head exchanger. They would require periodic cleaning. But unlike filters, you would not have to shut down the cooling system to do so. In addition, you don't have to worry about there being any sudden changes in the cooling capacity of the system so it should be much easier to plan and perform the cleaning.